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Clinical Microbiology Infection: Emerging Pathogens and Antimicrobial Resistance

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A special issue of Pathogens (ISSN 2076-0817). This special issue belongs to the section "Bacterial Pathogens".

Deadline for manuscript submissions: closed (15 December 2023) | Viewed by 15453

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Dr. Elvira Garza-González

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Department of Biochemistry and Molecular Medicine, School of Medicine, Autonomous University of Nuevo León, Monterrey 64460, Mexico
Interests: clinical microbiology; drug resistance; molecular epidemiology

Special Issue Information

Dear Colleagues,

In recent years, there has been global concern about the increasing incidence of emerging and re-emerging pathogens resistant to antimicrobials. These organisms include Gram-positive and Gram-negative bacteria, primarily found in, but not restricted to, the hospital environment. In this scenario, some strains are now resistant to most available antibiotics, new drug resistance mechanisms have been described, and strains have spread across different regions of the world.

This Special Issue will accept submissions which highlight reporting on emerging and re-emerging pathogens and antimicrobial resistance, including epidemiological aspects, the spread of high-risk clones, molecular mechanisms of antibiotic resistance and virulence, and increasing resistance to new and old antibiotics.

Dr. Elvira Garza-González
Guest Editor

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Keywords

drug resistance
reemergence of bacterial pathogens
emerging pathogens
antimicrobial resistance
clinical microbiology infection

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Published Papers (5 papers)

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Research

15 pages, 2078 KiB

Open AccessArticle

Clinical Outcomes of Third-Generation Cephalosporin Definitive Therapy for Bloodstream Infections Due to Enterobacterales with Potential AmpC Induction: A Single-Center Retrospective Study

by Gilles Vossius, Cécile Meex, Filip Moerman, Marie Thys, Marie Ernst, Marie-Eve Bourgeois, Léa Wagner, Thibaut Delahaye and Gilles Darcis

Pathogens 2023, 12(9), 1152; https://doi.org/10.3390/pathogens12091152 - 11 Sep 2023

Cited by 1 | Viewed by 1640

Abstract

The recommended therapy for severe infections caused by AmpC-inducible Enterobacterales (AmpC-E) typically involves cefepime or carbapenems. In an era of emerging resistance to these antimicrobials, we aim to assess the impact of third-generation cephalosporins (3GCs) vs. alternative antibiotics on clinical outcomes in bloodstream infections (BSIs) due to AmpC-E. We retrospectively included hospitalized adult patients with BSIs caused by 3GC-susceptible AmpC-E between 2012 and 2022, comparing the outcomes of 3GC and non-3GC definitive therapies. The primary outcome was overall treatment failure (OTF), encompassing 90-day all-cause mortality, 90-day reinfection, and 90-day readmission. Secondary outcomes comprised components of the OTF, in-hospital all-cause mortality, and length-of-stay. Within a total cohort of 353 patients, OTF occurred in 46.5% and 41.5% in the 3GC- and non-3GC-therapy groups, respectively (p = 0.36). The 3GC-therapy group exhibited a longer length-of-stay (38 vs. 21 days, p = 0.0003) and higher in-hospital mortality (23.3% vs. 13.4%, p = 0.019). However, the 90-day mortality, 90-day reinfection, and 90-day readmission were comparable between the therapy groups. Subgroup analyses involving high-risk AmpC-E and 3GC vs. standard-of-care yielded similar conclusions. Overall, our findings suggest that 3GC definitive therapy may not result in poorer clinical outcomes for the treatment of BSIs caused by AmpC-E. Full article

(This article belongs to the Special Issue Clinical Microbiology Infection: Emerging Pathogens and Antimicrobial Resistance)

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15 pages, 878 KiB

Open AccessArticle

Active Surveillance of Antimicrobial Resistance and Carbapenemase-Encoding Genes According to Sites of Care and Age Groups in Mexico: Results from the INVIFAR Network

by Fabian Rojas-Larios, Bernardo Alfonso Martínez-Guerra, Luis Esaú López-Jácome, Enrique Bolado-Martínez, María del Rosario Vázquez-Larios, María del Consuelo Velázquez-Acosta, Daniel Romero-Romero, Christian Daniel Mireles-Dávalos, Sandra Quintana-Ponce, José Manuel Feliciano-Guzmán, José Miguel Pérez-Hernandez, Yoselin Paola Correa-León, Eduardo López-Gutiérrez, Eduardo Rodriguez-Noriega, Esteban González-Díaz, Elena Victoria Choy-Chang, Juan Pablo Mena-Ramírez, Víctor Antonio Monroy-Colín, Alfredo Ponce-de-León-Garduño, Margarita Alcaraz-Espejel, Laura Karina Avilés-Benítez, Luís Javier Quintanilla-Cazares, Eloisa Ramírez-Alanís, Juan Manuel Barajas-Magallón, Cecilia Padilla-Ibarra, Maria Bertha Ballesteros-Silva, Noe Antonio Atanacio-Sixto, Cecilia Teresita Morales-de-la-Peña, Mario Galindo-Méndez, Talía Pérez-Vicelis, Guillermo Jacobo-Baca, Martha Irene Moreno-Méndez, María de la Luz Mora-Pacheco, Maricruz Gutiérrez-Brito, Xochitl Yadira Sánchez-Godínez, Norberta Vianey Navarro-Vargas, Luz Elena Mercado-Bravo, Alejandro Delgado-Barrientos, María Asunción Santiago-Calderón, Ismelda López-Ovilla, Alejandro Molina-Chavarria, Joaquín Rincón-Zuno, Rafael Franco-Cendejas, Sandra Miranda-Mauricio, Isabel Cristina Márquez-Avalos, Maribel López-García, Lizbeth Soraya Duarte-Miranda, Carlos Miguel Cetina-Umaña, Irma Elena Barroso-Herrera-y-Cairo, Laura Isabel López-Moreno and Elvira Garza-González Show full author list Hide full author list

Pathogens 2023, 12(9), 1144; https://doi.org/10.3390/pathogens12091144 - 7 Sep 2023

Cited by 7 | Viewed by 2496

Abstract

We analyzed the antimicrobial resistance (AMR) data of 6519 clinical isolates of Escherichia coli (n = 3985), Klebsiella pneumoniae (n = 775), Acinetobacter baumannii (n = 163), Pseudomonas aeruginosa (n = 781), Enterococcus faecium (n = 124), and Staphylococcus aureus (n = 691) from 43 centers in Mexico. AMR assays were performed using commercial microdilution systems (37/43) and the disk diffusion susceptibility method (6/43). The presence of carbapenemase-encoding genes was assessed using PCR. Data from centers regarding site of care, patient age, and clinical specimen were collected. According to the site of care, the highest AMR was observed in E. coli, K. pneumoniae, and P. aeruginosa isolates from ICU patients. In contrast, in A. baumannii, higher AMR was observed in isolates from hospitalized non-ICU patients. According to age group, the highest AMR was observed in the ≥60 years age group for E. coli, E. faecium, and S. aureus, and in the 19–59 years age group for A. baumannii and P. aeruginosa. According to clinical specimen type, a higher AMR was observed in E. coli, K. pneumoniae, and P. aeruginosa isolates from blood specimens. The most frequently detected carbapenemase-encoding gene in E. coli was bla_NDM (84%). Full article

(This article belongs to the Special Issue Clinical Microbiology Infection: Emerging Pathogens and Antimicrobial Resistance)

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12 pages, 304 KiB

Open AccessArticle

Insights into the Intersection of Biocide Resistance, Efflux Pumps, and Sequence Types in Carbapenem-Resistant Acinetobacter baumannii: A Multicenter Study

by Zeeshan Taj, Muhammad Hidayat Rasool, Mohsin Khurshid, Bilal Aslam and Muhammad Usman Qamar

Pathogens 2023, 12(7), 899; https://doi.org/10.3390/pathogens12070899 - 30 Jun 2023

Cited by 3 | Viewed by 2289

Abstract

Acinetobacter baumannii, a pathogenic bacterium acquired in hospitals, causes diverse infections in humans. Previous studies have reported resistance among A. baumannii strains, potentially selecting multi-drug-resistant variants. In Pakistan, research has primarily focused on carbapenem-resistant A. baumannii (CRAB) strains, overlooking the investigation of efflux pumps (EPs) and biocide resistance. This study aims to assess A. baumannii strains from five hospitals in Pakistan, focusing on antibiotic and biocide susceptibility, the impact of EP inhibitors on antimicrobial susceptibility, and the distribution of ARGs and STs. A total of 130 non-repeated Acinetobacter baumannii isolates were collected from five tertiary care hospitals in Pakistan and identified using API 20NE and multiplex PCR. Antimicrobial susceptibility testing utilized disc diffusion and broth microdilution assays, while biocide susceptibility was assessed with various agents. The impact of an efflux pump inhibitor (NMP) on antibiotic susceptibility was evaluated. PCR screening for ARGs and EPGs was followed by DNA sequencing validation. MLST was performed using the Pasteur scheme. Most isolates demonstrated resistance to tested antibiotics, with varying levels of susceptibility to biocides. All isolates exhibited the intrinsic class D β-lactamase bla_OXA-51, while acquired bla_OXA-23 was present in all CRAB isolates. Among EPs, adeJ, abeD, amvA, and aceI were prevalent in almost all isolates, with adeB found in 93% of isolates and adeG, adeT1, adeT2, and qacEΔ1 displaying lower prevalence ranging from 65% to 79%. The most common STs were ST589 and ST2, accounting for 28.46% and 25.38% of isolates, respectively, followed by ST642 at 12.6%. These findings indicate that A. baumannii strains in Pakistan are resistant to antibiotics (excluding colistin and tigecycline) and may be developing biocide resistance, which could contribute to the selection and dissemination of multi-drug-resistant strains. Full article

(This article belongs to the Special Issue Clinical Microbiology Infection: Emerging Pathogens and Antimicrobial Resistance)

13 pages, 2079 KiB

Open AccessArticle

Isolation and Identification of Multidrug-Resistant Klebsiella pneumoniae Clones from the Hospital Environment

by María Guadalupe Córdova-Espinoza, Silvia Giono-Cerezo, Erika Gabriela Sierra-Atanacio, Alejandro Escamilla-Gutiérrez, Eduardo Carrillo-Tapia, Laura Isabel Carrillo-Vázquez, Felipe Mendoza-Pérez, Martha Leyte-Lugo, Raquel González-Vázquez, Lino Mayorga-Reyes and Rosa González-Vázquez

Pathogens 2023, 12(5), 634; https://doi.org/10.3390/pathogens12050634 - 23 Apr 2023

Cited by 7 | Viewed by 3645

Abstract

Global dispersion, hospital outbreaks, and lineage relationships between emerging antibiotic-resistant strains such as Klebsiella pneumoniae are of public health interest. This study aimed to isolate and identify K. pneumoniae clones from third-level healthcare hospitals in Mexico to establish their multidrug-resistant phenotype, phylogeny, and prevalence. Biological and abiotic surface samples were used to isolate K. pneumoniae strains and to test their antibiotic susceptibility to classify them. The housekeeping genes: gapA, InfB, mdh, pgi, phoE, ropB, and tonB were used for multilocus sequence typing (MLST). Phylogenetic networks were constructed with 48 strains. Isolated strains (93) were mainly from urine and blood, 96% were resistant to ampicillin as expected, 60% were extended-spectrum β-lactamases (ESBL), 98% were susceptible to ertapenem and meropenem and 99% were susceptible to imipenem, 46% were multi-drug resistant (MDR), 17% were extensively-drug resistant (XDR), 1% were pan-drug resistant (PDR), and 36% were not classified. The tonB, mdh, and phoE genes were the most variable, and the InfB gene showed positive selection. The most prevalent sequence types (STs) were ST551 (six clones), ST405 (six clones), ST1088 (four clones), ST25 (four clones), ST392 (three clones), and ST36 (two clones). ST706 was PDR, and ST1088 clones were MDR; neither of these STs has been reported in Mexico. The strains analyzed were from different hospitals and locations; thus, it is important to maintain antibiotic surveillance and avoid clone dissemination to prevent outbreaks, adaptation to antibiotics, and the transmission of antibiotic resistance. Full article

(This article belongs to the Special Issue Clinical Microbiology Infection: Emerging Pathogens and Antimicrobial Resistance)

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20 pages, 4688 KiB

Open AccessArticle

Prevalence and Characterization of Salmonella Isolated from Chickens in Anhui, China

by Xuehuai Shen, Lei Yin, Anyun Zhang, Ruihong Zhao, Dongdong Yin, Jieru Wang, Yin Dai, Hongyan Hou, Xiaocheng Pan, Xiaomiao Hu, Danjun Zhang and Yongjie Liu

Pathogens 2023, 12(3), 465; https://doi.org/10.3390/pathogens12030465 - 16 Mar 2023

Cited by 18 | Viewed by 4790

Abstract

Salmonella is one of the most important zoonotic pathogens that can cause both acute and chronic illnesses in poultry flocks, and can also be transmitted to humans from infected poultry. The purpose of this study was to investigate the prevalence, antimicrobial resistance, and molecular characteristics of Salmonella isolated from diseased and clinically healthy chickens in Anhui, China. In total, 108 Salmonella isolates (5.66%) were successfully recovered from chicken samples (n = 1908), including pathological tissue (57/408, 13.97%) and cloacal swabs (51/1500, 3.40%), and S. Enteritidis (43.52%), S. Typhimurium (23.15%), and S. Pullorum (10.19%) were the three most prevalent isolates. Salmonella isolates showed high rates of resistance to penicillin (61.11%), tetracyclines (47.22% to tetracycline and 45.37% to doxycycline), and sulfonamides (48.89%), and all isolates were susceptible to imipenem and polymyxin B. In total, 43.52% isolates were multidrug-resistant and had complex antimicrobial resistance patterns. The majority of isolates harbored cat1 (77.78%), blaTEM (61.11%), and blaCMY-2 (63.89%) genes, and the antimicrobial resistance genes in the isolates were significantly positively correlated with their corresponding resistance phenotype. Salmonella isolates carry high rates of virulence genes, with some of these reaching 100% (invA, mgtC, and stn). Fifty-seven isolates (52.78%) were biofilm-producing. The 108 isolates were classified into 12 sequence types (STs), whereby ST11 (43.51%) was the most prevalent, followed by ST19 (20.37%) and ST92 (13.89%). In conclusion, Salmonella infection in chicken flocks is still serious in Anhui Province, and not only causes disease in chickens but might also pose a threat to public health security. Full article

(This article belongs to the Special Issue Clinical Microbiology Infection: Emerging Pathogens and Antimicrobial Resistance)

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